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Plotting Integration Values

This tutorial will illustrate to how to find the integration values of a proton 1-dimensional spectrum, as well as create a post-script file output using the vnmrj software.

 

  

Click File, Open, to select the data you wish to analyze. A previously recorded proton spectrum of ethyl-trans crotonate will be used as an example.

To automatically scale the spectrum type vsadj for vertical scale adjust.

To automatically phase the spectrum type aph for auto-phase.

After adjusting the spectrum, click the Show Integral Regions icon on the right side toolbar. Now click Process, then Integration in the left hand column. Then, finally Clear Integrals, because we wish to select the integrals manually.

Using the center mouse wheel scroll up or down to set the vertical scale so that the integral line is completely visible in the interface, then click Interactive Resets. You will now use the left mouse button to select each peak by clicking to the left, then to the right of each resonance.

Be sure to include the solvent peak and TMS, because everything that is not selected from this point forward is considered to be noise. If we ignored the solvent peak and TMS if would affect the baseline correction since they would be falsely considered noise. If you make a mistake selecting each peak during this process, click Clear Integrals then Interactive Resets once again to start over.

Now we will execute a baseline correction using the bc command with an argument of 3. Type bc(3). The argument corresponds to the order of the polynomial used for the baseline correction. For most cases an argument of 3 or 4 will be sufficient, but if you have a very distorted baseline you may need a higher order polynomial. It is important to keep in mind that smaller values like 3 or 4 generally produce acceptable results.

Now set the integration values by placing the cursor in the center of a resonance with a known number of corresponding protons. For the spectrum of ethyl trans-crotonate, we can assume that the resonance around 7ppm is caused by a methine, which has one bound proton. We can place the cursor in the center of this resonance (~7ppm), then set the integral area for 100, and click Set Integral Value.

structure of ethyl trans crotonate

We could also place the cursor in any other resonance and follow the same procedure setting the integral value accordingly. It can be assumed that the furthest upfield resonance corresponds to a methyl moiety, so the integration value would be set to 300 for the three protons of a methyl. The integration values are displayed should be very close to a ratio of 1:2:3 for one proton, two protons, and three protons respectively.

If the ratio is off from 100:200:300, this could be because while recording the data not enough time was set between transients. This is okay for simple molecules like ethyl trans-crotonate. But for more complicated molecules it is important to be careful when setting the time between scans.

To begin plotting the data click Plot in the left side column. Check the box next to the title Integral Values. Then click scaled, and ppm. To plot only the spectrum with integration values, click none under the Parameter heading. To choose to plot experimental parameters with the spectrum, click Basic or All.

To print the plotted spectra click Print

To save the plotted spectra as a post script file click Preview. This saves the plot in a format that can be edited and further annotated by illustrator, canvas, or any other similar software.

To email yourself a .pdf containing the plotted spectrum, first click File then AutoSave. Then click Preview, check the box next to email, and enter the email you would like to send the plot.

Last Updated: 3/5/17